The Full Cytosine-Cytosine Base Paring: Self-Assembly and Crystal Structure

The synthesis of self-assembly systems that can mimic partial biological behaviours require ingenious and delicate design. For decades, scientists are committed to exploring new base pairing patterns using hydrogen bonds directed self-assembly of nucleotides. A fundamental question is the adaptive circumstance of the recognition between base pairs, namely, how solvent conditions affect the domain of base pairs. Towards this question, three nucleotide complexes based on 2'-deoxycytidine-5'-monophosphate (dCMP) and cytidine-5'-monophosphate (CMP) were synthesized in different solvents and pH values, and an unusual cytosine-cytosine base paring pattern (named full C : C base pairing) has been successfully obtained. Systematic single crystal analysis and ¹ H NMR titration spectra have been performed to explore factors influencing the formation of base paring patterns. Moreover, supramolecular chirality of three complexes were studied using circular dichroism (CD) spectroscopy in solution and solid-state combined with crystal structure analysis.

Conformation Locking of the Pentose Ring in Nucleotide Monophosphate Coordination Polymers via π-π Stacking and Metal-Ion Coordination

The conformation of the pentose ring in nucleotides is extremely important and a basic problem in biochemistry and pharmaceutical chemistry. In this study, we used a strategy to regulate the conformation of pentose rings of nucleotides via the synergistic effect of metal-ion coordination and π-π stacking. Seven types of coordination complexes were developed and characterized using Fourier transform infrared spectroscopy, elemental analysis, thermogravimetric analysis, powder X-ray diffraction, ultraviolet-visible spectroscopy, 1H nuclear magnetic resonance spectroscopy, electrospray ionization mass spectrometry, and single-crystal X-ray diffraction. On the basis of two conformational parameters obtained from single-crystal structure analysis, i.e., the pseudorotation phase angle and degree of puckering, the exact conformation of the furanose ring in these coordination polymers was unequivocally determined. Crystallographic studies demonstrate that a short bridging ligand (4,4'-bipyridine) is conducive to the formation of a twist form, and long auxiliary ligands [1,2-bis(4-pyridyl)ethene and 4,4'-azopyridine] induce the formation of an envelope conformation. However, the longest auxiliary ligands [1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene] cannot limit the flexibility of a nucleotide. Our results demonstrated that the proposed strategy is universal and controllable. Moreover, the chirality of these coordination polymers was examined by combining the explanation of their crystal structures with solid-state circular dichroism spectroscopy measurements.

A Nanoporous Supramolecular Metal-Organic Framework Based on a Nucleotide: Interplay of the π···π Interactions Directing Assembly and Geometric Matching of Aromatic Tails

Self-assembly is the most powerful force for creating ordered supramolecular architectures from simple components under mild conditions. π···π stacking interactions have been widely explored in modern supramolecular chemistry as an attractive reversible noncovalent tool for the nondestructive fabrication of materials for different applications. Here, we report on the self-assembly of cytidine 5’-monophosphate (CMP) nucleotide and copper metal ions for the preparation of a rare nanoporous supramolecular metal-organic framework in water. π···π stacking interactions involving the aromatic groups of the ancillary 2,2’-bipyridine (bipy) ligands drive the self-assemblies of hexameric pseudo-amphiphilic [Cu6(bipy)6(CMP)2(µ-O)Br4]²⁺ units. Owing to the supramolecular geometric matching between the aromatic tails, a nanoporous crystalline phase with hydrophobic and hydrophilic chiral pores of 1.2 and 0.8 nanometers, respectively, was successfully synthesized. The encoded chiral information, contained on the enantiopure building blocks, is transferred to the final supramolecular structure, assembled in the very unusual topology 8T6. These kinds of materials, owing to chiral channels with chiral active sites from ribose moieties, where the enantioselective recognition can occur, are, in principle, good candidates to carry out efficient separation of enantiomers, better than traditional inorganic and organic porous materials.

Controllable synthesis of two adenosine 5'-monophosphate nucleotide coordination polymers via pH regulation: crystal structure and chirality

Two types of Cu(ii)-AMP-4,4'-bipy coordination polymers, {[Cu(AMP)(4,4'-bipy)(H₂O)₃]·5H₂O}n (1) and {[Cu₂(HAMP)₂(4,4'-bipy)₂(H₂O)₄]·2NO₃·11H₂O}n (2) (Na₂AMP = adenosine 5'-monophosphate disodium salt), were synthesised through pH control. X-ray single-crystal diffraction analysis revealed that 1 and 2 are one-dimensional (1D) coordinating coordination polymers. The nucleotide in 1 was not protonated whereas that in 2 was protonated. With the protonated NO₃^- in 2 entering the crystal lattice, it plays a role in balancing the charge. The chirality was studied using solid-state circular dichroism (CD) spectroscopy based on the analysis of crystal structures.

Studies on the structure and chirality of A-motif in adenosine monophosphate nucleotide metal coordination complexes

Structure and chirality of A-motif.

Multistimulus-Responsive Supramolecular Hydrogels Derived by in situ Coating of Ag Nanoparticles on 5'-CMP-Capped β-FeOOH Binary Nanohybrids with Multifunctional Features and Applications

The present manuscript reports the synthesis of multistimulus-responsive smart supramolecular hydrogels derived by in situ coating of silver nanoparticles (Ag NPs) on colloidal cytidine-5'-monophosphate-capped β-FeOOH nanohybrids (β-FeOOH@5'-CMP) under physiological conditions forming a polycrystalline building block (Ag-coated β-FeOOH@5'-CMP). The presence of Ag in the binary nanohybrids induces the puckering of ribose sugar, bringing a change in its conformation from C2'-endo to C3'-endo, which enhanced the supramolecular interactions among different moieties of other building blocks to construct a porous network of hydrogels in the self-assembly via the formation of a micellar structure. Such a supramolecular network in hydrogel is also evidenced by the reversible sol⇌gel transformation under multistimulus-responsiveness in a narrow range of pH, temperature, and sonication, as well as by the manifestation of rapid self-healing and injectability features. As-synthesized hydrogels exhibiting shear-thinning behavior under higher strain and converting back into the sol under low strain, suggests their potential for localized drug delivery. The presence of Ag NPs in the hydrogel enhanced its viscoelastic properties, % swelling (580) and loading capabilities (590 mg g^-1) for methylene blue (MB), and its controlled release over days (∼2-30) as a function of pH. It displayed excellent surface-enhanced Raman spectroscopy activity allowing to detect MB-like drug molecules at ≤10^-12 M. Thus, the as-synthesized hydrogels represent a unique superparamagnetic nanosystem consisting of all greener components (5'-CMP/β-FeOOH/Ag) with superior viscoelastic, sensing, and antimicrobial properties, displaying multistimulus-responsiveness (pH/temperature/sonication), thereby suggesting their vast potential for biomedical and environmental applications.

Crystal structure of catena-poly[diaqua-(μ2-4,4′-bipyridine-κ2 N:N′)-bis(2,3,4,5-tetrabromo-6-carboxybenzoato-κ1 O)-nickel(II)], C26H14Br8NiN2O10

C26H14Br8NiN2O10, orthorhombic, Pbcn (no. 60), a = 24.1740(4) Å, b = 11.3727(2) Å, c = 11.7918(2) Å, V = 3241.84(10 Å3, Z = 4, R gt(F) = 0.0300, wR ref(F 2) = 0.0804, T = 293 K.

Crystal structure of poly[diaqua-(μ2-4,4′-bipyridine-κ2 N:N′)-(μ2-3,4,5,6-tetrafluorophthalato-κ2 O:O′)nickel(II)], C18H12F4NiN2O6

C18H12F4NiN2O6, orthorhombic, Pccn (no. 56), a = 7.4650(2) Å, b = 10.6954(2) Å, c = 22.7513(5) Å, V = 1816.49(7) Å3, Z = 4, R gt(F) = 0.0304, wR ref(F 2) = 0.0898, T = 293 K.

Crystal structure of catena-poly[diaqua-bis(3,4,5,6-tetrabromo-carboxybenzoato-κ1O)-(μ2-4,4′-bipyridine-κ2N:N′)cobalt(II)], C26H14Br8CoN2O10

C26H14Br8CoN2O10, orthorhombic, Pbcn (no. 60), a = 24.3935(3) Å, b = 11.4505(1) Å, c = 11.7004(1) Å, V = 3268.13(6) Å3, Z = 4, Rgt(F) = 0.0313, wRref(F2) = 0.0819, T = 293 K.

Environmentally benign pH-responsive cytidine-5′-monophosphate molecule-mediated akaganeite (5′-CMP-β-FeOOH) soft supramolecular hydrogels induced by the puckering of ribose sugar with efficient loading/release capabilities

A novel synthetic protocol for environmentally benign 5′-CMP-β-FeOOH soft hydrogels exhibiting a rapid pH-responsive reversible sol–gel transition, efficient adsorption and slow release capabilities is reported.

Double layer zinc–UDP coordination polymers: structure and properties

Double layer Zn–UDP coordination polymers with potentially open sites can be used for heterogeneous fluorescent sensors of amino acids.

Supramolecular Assembly of Uridine Monophosphate (UMP) and Thymidine Monophosphate (TMP) with a Dinuclear Copper(II) Receptor

Understanding the intermolecular interactions between nucleotides and artificial receptors is crucial to understanding the role of nucleic acids in living systems. However, direct structural evidence showing precise interactions and bonding features of a nucleoside monophosphate (NMP) with a macrocycle-based synthetic molecule has not been provided so far. Herein, we present two novel crystal structures of uridine monophosphate (UMP) and thymidine monophosphate (TMP) complexes with a macrocycle-based dinuclear receptor. Structural characterization of these complexes reveals that the receptor recognizes UMP through coordinate-covalent interactions with phosphates and π-π stackings with nucleobases and TMP through coordinate-covalent interactions with phosphate groups. Furthermore, the receptor has been shown to effectively bind nucleoside monophosphates in the order of GMP > AMP > UMP > TMP > CMP in water at physiological pH, as investigated by an indicator displacement assay.

Cytosine-Cytosine Base-Pair Mismatch and Chirality in Nucleotide Supramolecular Coordination Complexes

The base-pair sequences are the foundation for the biological processes of DNA or RNA, and base-pair mismatch is very important to reveal genetic diseases and DNA rearrangements. However, the lack of well-defined structural information about base-pair mismatch is obstructing the investigation of this issue. The challenge is to crystallize the materials containing the base-pair mismatch. Engineering the small-molecule mimics or model is an effective strategy to solve this issue. Here, six cytidine-5'-monophosphate (CMP) and 2'-deoxycytidine-5'-monophosphate (dCMP) coordination polymers were reported containing cytosine-cytosine base-pair mismatch (i-motif), and their single-crystal structures and chiralities were studied. The precise control over the formation of the i-motif was demonstrated, in which the regulating of supramolecular interactions was achieved based on molecular design. In addition, the chiralities of these coordination polymers were investigated according to their crystal structures and solution- and solid-state circular dichroism spectroscopy.

Multicopper Laccase Mimicking Nanozymes with Nucleotides as Ligands

Using nanomaterials to achieve functional enzyme mimics (nanozymes) is attractive for both applied and fundamental research. Laccases are multicopper oxidases highly important for biotechnology and environmental remediation. In this work, we report an exceptionally simple yet functional laccase mimic based on guanosine monophosphate (GMP) coordinated copper. It forms an amorphous metal-organic framework (MOF) material. The ratio of copper and GMP is 3:4 as determined by isothermal titration calorimetry. It has excellent laccase-like activity and converts a diverse range of phenol containing substrates such as hydroquinone, naphthol, catechol and epinephrine. Comparative work shows that the activity is originated from guanosine coordination instead of phosphate binding in GMP. Cu²⁺ is required and cannot be substituted by other metal ions. At the same mass concentration, the Cu/GMP nanozyme has a higher V_max and similar K_m compared to the protein laccase. To achieve the same catalytic efficiency, the cost of the Gu/GMP is ∼2400-fold lower than that of laccase. The Cu/GMP is much more stable at extreme pH, high salt, high temperature and for long-term storage. This is one of the first laccase-mimicking nanozymes, which will find important applications in analytical chemistry, environmental protection, and biotechnology.

The first X-ray structure of a silver–nucleotide complex: interaction of ion Ag(i) with cytidine-5′-monophosphate

The synthesis and X-ray characterization of an unprecedented complex of Ag(i) with cytidine-5′-monophosphate (HCMP) is reported. The coordination of Ag(i) to HCMP is via both the N3 and O2 atoms of two cytosine moieties and the phosphate group, generating a MOF.

Unusual crystal structure and chirality of uridine 5′-monophosphate coordination polymer

The auxiliary ligand effect in the structure and charility of uridine 5′-monophosphate coordination polymer was investigated.

Controllable synthesis of nucleotide complex based on pH control: a small-molecule fluorescent probe as an auxiliary ligand to indicate the pre-organization of the nucleotide complex in solution

Different CMP-bpe-M(ii) (CMP = cytidine monophosphate, bpe = bis(4-pyridyl)ethylene, M(ii) = Mn(2+) and Co(2+)) complexes are synthesized controllably based on pH control and well studied by X-ray single-crystal diffraction analysis. Interestingly, the suitable pH conditions are explored by considering the pre-organization modes of CMP, bpe, and M(2+) in aqueous solution by fluorescence spectroscopy based on acid/basic titration. The organic base bpe serves as a small-molecule fluorescent probe to indicate the changes of pre-organization modes along with the changes of the solution acidity. Furthermore, a perfect self-complementary sugar-base hydrogen bond is first reported based on the crystal structure analysis in this work, and different chiralities and SHG activities of CMP-bpe-Mn(ii) complexes obtained at different pH values are studied.

Homochiral self-assembly of biocoordination polymers: anion-triggered helicity and absolute configuration inversion

The different natures of the weakly coordinating anions - triflate or perchlorate - in the Cu2+-mediated self-assembly of cytidine monophosphate nucleotide play a fundamental role in the homochiral resolution process, yielding one-dimensional copper(ii) coordination polymers of opposite helicity that can be easily inverted, in a reversible way, by changing the nature of the anion as revealed by circular dichroism experiments both in solution and in the solid state.

Temperature-induced one-dimensional chiral Ag(i) linear chains and left-handed 21 helices: DFT studies, luminescence and SHG response

Two pairs of chiral coordination polymers have been synthesized with the same materials at 25 and 90 °C, respectively.